DESCRIPTION

Conversion of measured intensities to structure factors is complicated by the
fact that background subtraction can result in negative intensities for weak
reflections. CTRUNCATE is a new CCP4 program, intended ultimately to replace
the original TRUNCATE program, which uses Bayesian statistics to calculate
positive structure factors from negative input intensities. Small positive
intensities are also boosted by the conversion process. The algorithm used is
that of French and Wilson.

In addition, CTRUNCATE calculates a number of statistics from the intensity
data, such as moments, cumulative intensity distributions and the Wilson
plot. When output in graphical form, these can be used to assess data quality
and to check for possible twinning.

CTRUNCATE looks for anisotropy in the data and performs anisotropy
correction. A test for translational NCS is also performed. Two methods are
used to test for twinning: Yeates' H test and Padilla and Yeates L test. The
twinning tests, as well as the moments and cumulative intensity plots are done
using data which has been corrected for anisotropy. However the output
structure factors and the Wilson plot use uncorrected data. Should tNCS or
twinning be found a flat prior based upon the same approximations as the
Wilson prior is applied.

INPUT/OUTPUT FILES

-hklin filename

(Compulsory) Input mtz file name. '-mtzin' is accepted as an alternative to
'-hklin'.

-hklout filename

-seqin sequence file name

Input sequence file in any common format (e.g. pir, fasta), used for scaling.

KEYWORDED INPUT

-colin column label

Column names for mean intensity data. If only anomalous data
is input, then only the anomalous data will be considered.

-colano column label

Column names for anomalous data. Both positive and negative names need to
be specified e.g. '/*/*/[I(+),SIGI(+),I(-),SIGI(-)]'.
If column names for anomalous data are not specified, the program will only
consider mean data.

-colout column label

Identifier to be appended to output column names.

-nres number of residues

Specifies the number of residues in the asymmetric unit for scaling
purposes. If not used and an input sequence file is not provided, the number
of residues will be estimated assuming 50% solvent content.

-no-aniso

Anisotropy correction will not be performed.

-amplitudes

Input data is structure factors rather than intensities.

-comp nucleic

Use DNA/RNA reference curve. The reference curve derived from 65
resonably high resolution intensities and structure factors from the PDB
and nucleic acid data bank.

-prior WILSON or FLAT

Force use of WILSON or FLAT prior.

-freein colname

Retain the the freeR column. Default colname is '/*/*/[FreeR_flag]'

Release Notes

1.13.0
- follow lead of K.Diederichs and extend tabulated range for truncate procedure to -37
(this is were R calculation becomes unstable for centric reflections)

1.12.5
- use range for anomalous limits rather than monatomical decrease